tbuckley/cabot-search huggingface dataset:
A practical toolbox for the effective transition of adolescents and young adults with asthma and allergies: An <scp>EAACI</scp> position paper
Authors: Marta Vazquez‐Ortiz, Claudia Gore, Cherry Alviani, Elizabeth Angier, Katharina Blumchen, Pasquale Comberiati, Bettina Duca, Audrey DunnGalvin, Teresa Garriga‐Baraut, M. Hazel Gowland, Britt Egmose, Rebecca Knibb, Ekaterina Khaleva, Charlotte G. Mortz, Oliver Pfaar, Helena Pite, Marcia Podesta, Alexandra F. Santos, Silvia Sanchez‐Garcia, Frans Timmermans, Graham Roberts
Journal: Allergy (2022)

Adolescence is a critical stage of rapid biological, emotional and social change and development. Adolescents and young adults (AYA) with asthma and allergies need to develop the knowledge and skills to self-manage their health independently. Healthcare professionals (HCP), parents and their wider network play an essential role in supporting AYA in this process. Previous work showed significant limitations in transition care across Europe. In 2020, the first evidence-based guideline on effective transition for AYA with asthma and allergies was published by EAACI.We herein summarize practical resources to support this guideline's implementation in clinical practice.For this purpose, multi-stakeholder Task Force members searched for resources in peer review journals and grey literature. These resources were included if relevant and of good quality and were pragmatically rated for their evidence-basis and user friendliness.Resources identified covered a range of topics and targeted healthcare professionals, AYA, parents/carers, schools, workplace and wider community. Most resources were in English, web-based and had limited evidence-basis.This position paper provides a valuable selection of practical resources for all stakeholders to support effective transitional care for AYA with asthma and allergies. Future research should focus on developing validated, patient-centred tools to further assist evidence-based transition care.
Free-energy pragmatics: Markov blankets don't prescribe objective ontology, and that's okay
Authors: Inês Hipólito, Thomas van Es
Journal: Behavioral and Brain Sciences (2022)

Abstract We target the ontological and epistemological ramifications of the proposed distinction between Friston and Pearl blankets. We emphasize the need for empirical testing next to computational modeling. A peculiar aspect of the free energy principle (FEP) is its purported support of radically opposed ontologies of the mind. In our view, the objective ontological aspiration itself should be rejected for a pragmatic instrumentalist view.
Maternal heated tobacco product use during pregnancy and allergy in offspring
Authors: Masayoshi Zaitsu, Kenta Kono, Yoshihiko Hosokawa, Manabu Miyamoto, Keiko Nanishi, Sumiyo Okawa, Shinji Niki, Kyo Takahashi, Shigemi Yoshihara, Gen Kobashi, Takahiro Tabuchi
Journal: Allergy (2022)

Little is known about the association between maternal use of heated tobacco products (HTPs) during pregnancy and the onset of allergy among offspring. This study aimed to determine whether maternal HTP smoking is associated with allergy in their offspring and to evaluate the potential dose-response association.
Return of the math: Markov blankets, dynamical systems theory, and the bounds of mind
Authors: Lincoln John Colling
Journal: Behavioral and Brain Sciences (2022)

Abstract Bruineberg and colleagues highlight work using Markov blankets to demarcate the bounds of the mind. This echoes earlier attempts to demarcate the bounds of the mind from a dynamical systems perspective. Advocates of mechanistic explanation have challenged the dynamical approach to independently motivate the application of the formalism, a challenge that Markov blanket theorists must also meet.
Markov blankets: Realism and our ontological commitments
Authors: Danielle J. Williams
Journal: Behavioral and Brain Sciences (2022)

Abstract The authors argue that their target is orthogonal to the realism and instrumentalist debate. I argue that it is born directly from it. While the distinction is helpful in illuminating how some ontological commitments demand a theory of implementation, it's less clear whether different views cleanly map onto the epistemic and metaphysical uses defined in the paper.
The emperor has no blanket!
Authors: Vicente Raja, Edward Baggs, Anthony Chemero, Michael L. Anderson
Journal: Behavioral and Brain Sciences (2022)

Abstract While we applaud Bruineberg et al.'s analysis of the differences between Markov blankets and Friston blankets, we think it is not carried out to its ultimate consequences. There are reasons to think that, once Friston blankets are accepted as a theoretical construct, they do not do the work proponents of free energy principle (FEP) attribute to them. The emperor is indeed naked.
BACH2 restricts NK cell maturation and function, limiting immunity to cancer metastasis
Authors: Charlotte J. Imianowski, Sarah K. Whiteside, Teresa Lozano, Alexander C. Evans, Jayme D. Benson, Christina J.F. Courreges, Firas Sadiyah, Colleen M. Lau, Nordin D. Zandhuis, Francis M. Grant, Martijn J. Schuijs, Panagiota Vardaka, Paula Kuo, Elizabeth J. Soilleux, Jie Yang, Joseph C. Sun, Tomohiro Kurosaki, Klaus Okkenhaug, Timotheus Y.F. Halim, Rahul Roychoudhuri
Journal: The Journal of Experimental Medicine (2022)

Natural killer (NK) cells are critical to immune surveillance against infections and cancer. Their role in immune surveillance requires that NK cells are present within tissues in a quiescent state. Mechanisms by which NK cells remain quiescent in tissues are incompletely elucidated. The transcriptional repressor BACH2 plays a critical role within the adaptive immune system, but its function within innate lymphocytes has been unclear. Here, we show that BACH2 acts as an intrinsic negative regulator of NK cell maturation and function. BACH2 is expressed within developing and mature NK cells and promotes the maintenance of immature NK cells by restricting their maturation in the presence of weak stimulatory signals. Loss of BACH2 within NK cells results in accumulation of activated NK cells with unrestrained cytotoxic function within tissues, which mediate augmented immune surveillance to pulmonary cancer metastasis. These findings establish a critical function of BACH2 as a global negative regulator of innate cytotoxic function and tumor immune surveillance by NK cells.
Making reification concrete: A response to Bruineberg et al.
Authors: Mel Andrews
Journal: Behavioral and Brain Sciences (2022)

Abstract The principal target of this article is the reification Bruineberg et al. perceive of formalism within the literature on the variational free energy minimization (VFEM) framework. The authors do not provide a definition of reification, as none yet exists. Here I offer one. On this definition, the objects of the authors' critiques fall short of full-blown reification – as do the authors themselves.
Sex differences in lymphoma incidence and mortality by subtype: A population‐based study
Authors: Cecilia Radkiewicz, Johanna B. Bruchfeld, Caroline E. Weibull, Mathias L. Jeppesen, Henrik Frederiksen, Mats Lambe, Lasse Jakobsen, Tarec C. El‐Galaly, Karin E. Smedby, Tove Wästerlid
Journal: American Journal of Hematology (2022)

It is well established that the male sex is associated with increased risk for, as well as poorer survival of, most cancers. A similar pattern has been described in lymphomas but has not yet been comprehensively assessed. In this nationwide population-based cohort study, we used the Swedish Lymphoma Register to investigate sex differences in lymphoma subtype incidence and excess mortality in adults (age 18-99) diagnosed in 2000-2019. Male-to-female incidence rate ratios (IRRs) and excess mortality ratios (EMRs) adjusted for age and calendar year were predicted using Poisson regression. We identified 36 795 lymphoma cases, 20 738 (56.4%) in men and 16 057 (43.6%) in women. Men were at significantly higher risk of 14 out of 16 lymphoma subtypes with IRRs ranging from 1.15 (95% confidence interval [CI] 1.09-1.22) in follicular lymphoma to 5.95 (95% CI 4.89-7.24) in hairy cell leukemia. EMRs >1 were seen in 13 out of 16 lymphoma subtypes indicating higher mortality in men, although only statistically significant for classical Hodgkin lymphoma 1.26 (95% CI 1.04-1.54), aggressive lymphoma not otherwise specified 1.29 (95% CI 1.08-1.55), and small lymphocytic lymphoma 1.52 (95% CI 1.11-2.07). A corresponding analysis using data from the Danish Lymphoma Register was performed with comparable results. In conclusion, we demonstrate a significantly higher incidence and trend toward higher mortality in men for most lymphoma subtypes. Future studies with large patient material that include detailed clinicopathological prognostic factors are warranted to further delineate and explain sex differences in lymphoma survival to enable optimal management of lymphoma patients regardless of sex.
Practical implications from distinguishing between Pearl blankets and Friston blankets
Authors: Stephen Fox
Journal: Behavioral and Brain Sciences (2022)

Abstract Analysis provided in The Emperor's New Markov Blankets reveals that there is limited potential for practical application of Pearl and Friston blankets. However, Bruineberg and colleagues' analysis includes a simple diagram that has potential to better enable shared understanding of interactions between free energy principle constructs during the design and implementation of biosocial–technical systems.
Fellowships, Grants, Awards
Journal: JNCI Journal of the National Cancer Institute (1994)

Journal Article Fellowships, Grants, Awards Get access JNCI: Journal of the National Cancer Institute, Volume 86, Issue 7, 6 April 1994, Pages 566–567, https://doi.org/10.1093/jnci/86.7.566 Published: 06 April 1994
Facile Fabrication of Injectable Alginate and Poly(3,4‐ethylenedioxythiophene)‐Based Soft Electrodes toward the Goal of Neuro‐Regenerative Applications
Authors: Ivana Perkucin, Kylie S. K. Lau, Tianhao Chen, Stephanie N. Iwasa, Hani E. Naguib, Cindi M. Morshead
Journal: Advanced Healthcare Materials (2022)

Resident brain neural precursor cells (NPCs) are electrosensitive cells that respond to electric field application by proliferating, differentiating, and undergoing rapid and directed cathodal migration. Harnessing NPC potential is a promising strategy to facilitate neural repair following injury or disease. The use of electric fields to activate NPCs is limited by current electrode designs which are typically made of conductive metals that are stiff and can lead to neuroinflammation following implantation, in part due to the mechanical mismatch between physiological conditions and material. Herein, the design of a novel, injectable biobased soft electrode with properties suitable for electrical stimulation in vivo is explored. The recent interest in using biologically derived polymers which are relatively abundant and afford economic feasibility have been built upon. Sodium alginate is utilized to form soft hydrogels, thereby addressing the issue of mechanical mismatch, and the conductive polymer, poly(3,4-ethylenedioxythiophene) (PEDOT), to generate an innovative new material. It is demonstrated that the optimized alginate PEDOT blend matches the modulus of the brain and is suitable for injection and is not cytotoxic to neural cells. Furthermore, in vivo studies demonstrate minimal activation of inflammatory cells upon implantation in the brain compared to classically used platinum-based electrodes.
Epidemiology Evidence for Health Effects of 150 per- and Polyfluoroalkyl Substances: A Systematic Evidence Map
Authors: Elizabeth G. Radke, J. Michael Wright, Krista Christensen, Cynthia J. Lin, Alexandra E. Goldstone, Courtney Lemeris, Kristina A. Thayer
Journal: Environmental Health Perspectives (2022)

Background: Per- and polyfluoroalkyl substances (PFAS) comprise a large class of chemicals with widespread use and persistence in the environment and in humans; however, most of the epidemiology research has focused on a small subset. Objectives: The aim of this systematic evidence map (SEM) is to summarize the epidemiology evidence on approximately 150 lesser studied PFAS prioritized by the EPA for tiered toxicity testing, facilitating interpretation of those results as well as identification of priorities for risk assessment and data gaps for future research. Methods: The Populations, Exposure, Comparators, and Outcomes (PECO) criteria were intentionally broad to identify studies of any health effects in humans with information on associations with exposure to the identified PFAS. Systematic review methods were used to search for literature that was screened using machine-learning software and manual review. Studies meeting the PECO criteria underwent quantitative data extraction and evaluation for risk of bias and sensitivity using the Integrated Risk Information System approach. Results: 193 epidemiology studies were identified, which included information on 15 of the PFAS of interest. The most commonly studied health effect categories were metabolic (n=37), endocrine (n=30), cardiovascular (30), female reproductive (n=27), developmental (n=26), immune (n=22), nervous (n=21), male reproductive (n=14), cancer (n=12), and urinary (n=11) effects. In study evaluation, 120 (62%) studies were considered High/Medium confidence for at least one outcome. Discussion: Most of the PFAS in this SEM have little to no epidemiology data available to inform evaluation of potential health effects. Although exposure to the 15 PFAS that had data was fairly low in most studies, these less-studied PFAS may be used as replacements for "legacy" PFAS, leading to potentially greater exposure. It is impractical to generate epidemiology evidence to fill the existing gaps for all potentially relevant PFAS. This SEM highlights some of the important research gaps that currently exist. https://doi.org/10.1289/EHP11185
Clinical and laboratory features of patients diagnosed with alpha‐gal syndrome—2010–2019
Authors: Alison M. Binder, Dena Cherry‐Brown, Brad J. Biggerstaff, Emma S. Jones, Claire L. Amelio, Charles B. Beard, Lyle R. Petersen, Gilbert J. Kersh, Scott P. Commins, Paige A. Armstrong
Journal: Allergy (2022)

Alpha-gal syndrome (AGS) is an IgE-mediated allergy to galactose-alpha-1,3-galactose. Clinical presentation ranges from hives to anaphylaxis; episodes typically occur 2-6 h after exposure to alpha-gal-containing products. In the United States, lone star tick bites are associated with the development of AGS. To characterize features of AGS, we evaluated a cohort of patients presenting for care at the University of North Carolina, focusing on symptoms, severity, and identifying features unique to specific alpha-gal-containing product exposures.We performed a chart review and descriptive analysis of 100 randomly selected patients with AGS during 2010-2019.Median age at onset was 53 years, 56% were female, 95% reported White race, 86% reported a history of tick bite, and 75% met the criteria for anaphylaxis based on the involvement of ≥2 organ systems. Those reporting dairy reactions were significantly less likely to report isolated mucocutaneous symptoms (3% vs. 24%; ratio [95% CI]: 0.1 [0.1, 0.3]) than those who tolerated dairy, and were more likely to report gastrointestinal symptoms (79% vs. 59%; ratio [95% CI]: 1.3 [0.7, 2.6]), although this difference was not statistically significant. Dairy-tolerant patients demonstrated higher alpha-gal sIgE titers (as a percentage of total IgE) than dairy-reactive patients (GM 4.1 [95% CI: 2.7, 6.1] vs. GM 2.5 [95% CI: 1.3, 4.8], respectively; ratio -1.6 [95% CI: -1.0, 3.9]).While tick exposure is common in the southern United States, nearly all AGS patients reported a tick bite. Gastrointestinal symptoms were prominent among those reporting reactions to dairy. Anaphylaxis was common, underscoring the severity and need to raise awareness of AGS among patients and providers.
Moving to More Evidence-Based Primary Care Encounters
Authors: Michael J. Barry, Chien-Wen Tseng
Journal: JAMA (2022)

This Viewpoint discusses ways in which free time during patient visits, resulting from removal of tradition- and reimbursement-driven care in favor of more evidence-based care, could be used to achieve better health outcomes based on recommendations from the US Preventive Services Task Force evidence-based preventive care.
Maps and territories, smoke, and mirrors
Authors: Karl Friston
Journal: Behavioral and Brain Sciences (2022)

Abstract It is a pleasure to comment on Bruineberg et al. – who raise some interesting questions of a philosophical and technical nature. I will try to answer three questions posed by the authors. Are Pearl and Friston blankets different things? Are Markov blankets used in an ontological sense? Is there a privileged Markov blanket?
Reply
Authors: Francesco Vizzutti, Ciro Celsa, Salvatore Battaglia, Roberto Miraglia, Marco Enea, Fabio Marra, Cristian Caporali, Calogero Cammà, Filippo Schepis
Journal: Hepatology (2022)

Vizzutti, Francesco; Celsa, Ciro; Battaglia, Salvatore; Miraglia, Roberto; Enea, Marco; Marra, Fabio; Caporali, Cristian; Cammà, Calogero; Schepis, Filippo Author Information
Scientific realism about Friston blankets without literalism
Authors: Julian Kiverstein, Michael Kirchhoff
Journal: Behavioral and Brain Sciences (2022)

Abstract Bruineberg and colleagues' critique of Friston blankets relies on what we call the “literalist fallacy”: the assumption that in order for Friston blankets to represent real boundaries, biological systems must literally possess or instantiate Markov blankets. We argue that it is important to distinguish a realist view of Friston blankets from the literalist view of Bruineberg and colleagues’ critique.
Diabetes and Obesity in Down Syndrome Across the Lifespan: A Retrospective Cohort Study Using U.K. Electronic Health Records
Authors: Aisha A. Aslam, R. Asaad Baksh, Sarah E. Pape, Andre Strydom, Martin C. Gulliford, Li F. Chan, Yann Herault, Andre Strydom, Li Chan, Marie-Claude Potier, Johannes Beckers, Pietro Liò, Mara Dierssen
Journal: Diabetes Care (2022)

Down syndrome (DS) is the most common form of chromosomal trisomy. Genetic factors in DS may increase the risk for diabetes. This study aimed to determine whether DS is associated with an increased incidence of diabetes and the relationship with obesity across the life span compared with control patients.
Spatiotemporal constraints of causality: Blanket closure emerges from localized interactions between temporally separable subsystems
Authors: Casper Hesp
Journal: Behavioral and Brain Sciences (2022)

In this commentary, I first acknowledge points of common ground with the target article by Bruineberg and colleagues. Then, I consider how certain ambiguities could be resolved by considering spatiotemporal constraints on causality. In particular I show how blanket closure emerges from localized interactions between temporally separable subsystems, and how this points to valuable directions of future research. Finally, I close with a process note discussing the allegorical implications of the authors' creative title.
A continuity of Markov blanket interpretations under the free-energy principle
Authors: Anil Seth, Tomasz Korbak, Alexander Tschantz
Journal: Behavioral and Brain Sciences (2022)

Abstract Bruineberg and colleagues helpfully distinguish between instrumental and ontological interpretations of Markov blankets, exposing the dangers of using the former to make claims about the latter. However, proposing a sharp distinction neglects the value of recognising a continuum spanning from instrumental to ontological. This value extends to the related distinction between “being” and “having” a model.
Enough blanket metaphysics, time for data-driven heuristics
Authors: Wiktor Rorot, Tomasz Korbak, Piotr Litwin, Marcin Miłkowski
Journal: Behavioral and Brain Sciences (2022)

Bruineberg and colleagues criticisms' have been received but downplayed in the free energy principle (FEP) literature. We strengthen their points, arguing that Friston blanket discovery, even if tractable, requires a full formal description of the system of interest at the outset. Hence, blanket metaphysics is futile, and we postulate that researchers should turn back to heuristic uses of Pearl blankets.
Does the metaphysical dog wag its formal tail? The free-energy principle and philosophical debates about life, mind, and matter
Authors: Wanja Wiese
Journal: Behavioral and Brain Sciences (2022)

Abstract According to Bruineberg and colleagues, philosophical arguments on life, mind, and matter that are based on the free-energy principle (FEP) (1) essentially draw on the Markov blanket construct and (2) tend to assume that strong metaphysical claims can be justified on the basis of metaphysically innocuous formal assumptions provided by FEP. I argue against both (1) and (2).
Blankets, heat, and why free energy has not illuminated the workings of the brain
Authors: Donald Spector, Daniel Graham
Journal: Behavioral and Brain Sciences (2022)

Abstract What can we hope to learn about brains from the free energy principle? In adopting the “primordial soup” physical model, Bruineberg et al. perpetuate the unsupported notion that the free-energy principle has a meaningful physical – and neuronal – interpretation. We examine how minimization of free energy arises in physical contexts, and what this can and cannot tell us about brains.
Errors in Supplement
Authors: Mytien Nguyen, Mayur Desai, Dowin Boatright
Journal: JAMA Pediatrics (2022)

Nazeeh Hanna, MD; Ari Heffes-Doon, MD; Xinhua Lin, PhD; Claudia Manzano De Mejia, MD; Bishoy Botros, BS; Ellen Gurzenda, BS; Amrita Nayak, MD
Markov blankets do not demarcate the boundaries of the mind
Authors: Richard Menary, Alexander J. Gillett
Journal: Behavioral and Brain Sciences (2022)

Abstract We agree with Bruineberg and colleagues' main claims. However, we urge for a more forceful critique by focusing on the extended mind debate. We argue that even once the Pearl and Friston versions of the Markov blanket have been untangled, that neither is sufficient for tackling and resolving the question of demarcating the boundaries of the mind.
Nothing but a useful tool? (F)utility and the free-energy principle
Authors: Matteo Colombo
Journal: Behavioral and Brain Sciences (2022)

Abstract Bruineberg and collaborators distinguish three philosophical positions about the status of Markov blankets in the context of active inference modelling, namely: literalism, realism, and instrumentalism. They criticize the first two positions and suggest that instrumentalism is “less problematic but also less interesting” (sect. 6.1.2, para. 5) Here, I sketch how literalists and realists might reply to Bruineberg et al.'s criticisms, and I explain why instrumentalism is more interesting and contentious than what Bruineberg and collaborators suggest.
Update: Outbreak of Acute Febrile Illness Among Athletes Participating in Eco-Challenge-Sabah 2000--Borneo, Malaysia, 2000
Journal: JAMA (2001)

During September 7-11, 2000, CDC was notified by the Idaho Department of Health, the Los Angeles County Department of Health Services, and the GeoSentinel Global Surveillance Network of at least 20 cases of acute febrile illness in three countries; all ill patients had participated in the Eco-Challenge-Sabah 2000 multisport expedition race in Borneo, Malaysia, during August 21-September 3, 2000. Participants included athletes from 29 U.S. states and 26 countries. This report updates the ongoing investigation of this outbreak through December 2, which suggests that Leptospira were the cause of illness and that water from the Segama River was the primary source of infection. Participants in adventure sports and exotic tourism should be aware of potential exposure to unusual and emerging infectious agents.